In total, 25 clones of Vitis vinifera `Pinot noir' and 22 clones of `Chardonnay' were analyzed with 100 microsatellite markers, selected from an initial screening of 228 markers. Of the 100 markers, 17 detected polymorphism within one or both of the cultivars. In `Pinot noir', 15 polymorphic markers detected 15 different genotypes, uniquely distinguished 12 clones out of the 25 and separated the remaining 13 clones into 3 groups. In `Chardonnay', 9 polymorphic markers detected 9 genotypes and uniquely distinguished 6 clones out of the 22. The remaining 16 clones were separated into 3 groups. For markers that were polymorphic in `Pinot noir' and `Chardonnay', none of the variant alleles were common to both cultivars. It is inferred from this result that the natural cross that produced `Chardonnay' probably occurred when `Pinot' was still relatively young. Many of the variant genotypes were expressed as three alleles. Further analysis revealed the presence of chimeras in which the third allele was present in leaf but not root or wood tissues, confirming that the grape apical meristem is functionally two-layered. Some clones that share the same microsatellite genotype are documented to have originated in the same locality, suggesting that the origins of undocumented clones may be traced by comparing their microsatellite genotypes with those of well-documented clones. Because clones of `Pinot noir' and `Chardonnay' are often visually indistinguishable, microsatellite genotyping may also be useful to detect identification errors in collections and nurseries.
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